|
| Status |
Public on Jun 02, 2016 |
| Title |
HCT116-Day42-HCG/GCH |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: male
cell line: HCT116
time point: day 42
treatment: 5-Aza-CdR
|
| Treatment protocol |
HCT116 cells were treated for 24h with 0.3uM 5-Aza-CdR
|
| Growth protocol |
HCT116 cells were cultured in McCoy5A media supplemented with 10% FBS and penicillin/streptomycin at 37C/5%CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were trypsinized and washed with PBS. Nuclei were isolated and treated with 300 U of M.CvIPI, a GpC methyltransferase which can methylate accessible GpC sites without affecting CpG information (Kelly et al 2012)
WGBS libraries were prepared based on previously described (Berman et al 2012) and according to Illumina's recommendation.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
NOMe-seq
|
| Data processing |
genomic alignment for paired-end reads were done using MAQ with the -c bisulfite mode
Low quality reads and improperly paired reads were filtered out
Methylation calling of CpG and GpC was done using Bis-SNP (Liu et al 2011)
Genome_build: hg19
Supplementary_files_format_and_content: Methylation value of CG and GC sites were extacted and bigwig files were generated
|
| |
|
| Submission date |
Apr 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jessica Charlet |
| E-mail(s) |
jessicacharlet@hotmail.com
|
| Organization name |
USC Keck School of Medicine
|
| Department |
Norris Cancer Center
|
| Lab |
Peter Jones's lab.
|
| Street address |
1441 Eastlake Avenue
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE68046 |
A novel bivalent chromatin state exists at enhancers |
|
| Relations |
| BioSample |
SAMN03492246 |
| SRA |
SRX1000195 |
